A novel computational approach to the silencing of Sugarcane Bacilliform Guadeloupe A Virus determines potential host-derived MicroRNAs in sugarcane (Saccharum officinarum L.)
文献类型： 外文期刊
作者： Ashraf, Fakiha 1 ; Ashraf, Muhammad Aleem 2 ; Hu, Xiaowen 4 ; Zhang, Shuzhen 1 ;
作者机构： 1.Chinese Acad Trop Agr Sci, Inst Trop Biosci & Biotechnol, Haikou, Hainan, Peoples R China
2.Chinese Acad Trop Agr Sci, Haikou Expt Stn, Haikou, Hainan, Peoples R China
3.Islamia Univ Bahawalpur, Univ Coll Agr & Environm Sci, Dept Plant Breeding & Genet, Baghdad Ul Jadeed Campus, Bahwalpur, Pakistan
4.Chinese Acad Trop Agr Sci, Zhanjiang Expt Stn, Zhanjiang, Guandong, Peoples R China
关键词： Computational algorithms; R language; miRNA; Saccharum officinarum; Sugarcane Bacilliform Guadeloupe A Virus; Target prediction; Gene silencing; miRanda; Virus-host interaction; RNA interference
期刊名称：PEERJ （ 影响因子：2.984； 五年影响因子：3.369 ）
ISSN： 2167-8359
年卷期： 2020 年 8 卷
页码：
收录情况： SCI
摘要： Sugarcane Bacilliform Guadeloupe A Virus (SCBGAV, genus Badnavirus, family Caulimoviridae) is an emerging, deleterious pathogen of sugarcane which presents a substantial barrier to producing high sugarcane earnings. Sugarcane bacilliform viruses (SCBVs) are one of the main species that infect sugarcane. During the last 30 years, significant genetic changes in SCBV strains have been observed with a high risk of disease incidence associated with crop damage. SCBV infection may lead to significant losses in biomass production in susceptible sugarcane cultivars. The circular, double-stranded (ds) DNA genome of SCBGAV (7.4 Kb) is composed of three open reading frames (ORFs) on the positive strand that replicate by a reverse transcriptase. SCBGAV can infect sugarcane in a semipersistent manner via the insect vectors sugarcane mealybug species. In the current study, we used miRNA target prediction algorithms to identify and comprehensively analyze the genome-wide sugarcane (Saccharum officinarum L.)-encoded microRNA (miRNA) targets against the SCBGAV. Mature miRNA target sequences were retrieved from the miRBase (miRNA database) and were further analyzed for hybridization to the SCBGAV genome. Multiple computational approaches-including miRNA-target seed pairing, multiple target positions, minimum free energy, target site accessibility, maximum complementarity, pattern recognition and minimum folding energy for attachments-were considered by all algorithms. Among them, sof-miR396 was identified as the top effective candidate, capable of targeting the vital ORF3 of the SCBGAV genome. miRanda, RNA22 and RNAhybrid algorithms predicted hybridization of sof-miR396 at common locus position 3394. The predicted sugarcane miRNAs against viral mRNA targets possess antiviral activities, leading to translational inhibition bymRNAcleavage. Interaction network of sugarcane-encoded miRNAs with SCBGAV genes, created using Circos, allow analyze new targets. The finding of the present study acts as a first step towards the creation of SCBGAV-resistant sugarcane through the expression of the identified miRNAs.
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